From 8ff50fe6b48d9855c887b718547a8d4802e6ccba Mon Sep 17 00:00:00 2001 From: Munyoki Kilyungi Date: Fri, 19 Aug 2022 00:10:30 +0300 Subject: Add gn:traitId and gn:publicationId. In GeneNetwork, a phenonytpe is currently identified by it's ID (primary key of the table from MariaDB). The only way to relate it to a publication is through a publication ID. This is important because there are some publications with a NULL value for "pubmed ID" and as such without the publication ID, some data is lost as there's no way to point to publication with a NULL "pubmed ID." * dump.scm (dump-publish-xref): Define gn:traitId and gn:publicationId. Signed-off-by: Arun Isaac --- dump.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/dump.scm b/dump.scm index 2a893ae..439f9e2 100755 --- a/dump.scm +++ b/dump.scm @@ -489,7 +489,11 @@ must be remedied." (gn:phenotypeOfSpecies rdfs:domain gn:phenotype) (gn:phenotypeOfSpecies rdfs:range gn:species)) (triples (phenotype-id->id (field PublishXRef PhenotypeId)) - (set gn:phenotypeOfSpecies (inbred-set-name->id (field InbredSet Name))))) + (set gn:phenotypeOfSpecies (inbred-set-name->id (field InbredSet Name))) + (set gn:traitId (field PublishXRef id)) + (set gn:publicationId + (string->identifier "publication" + (number->string (field PublishXRef PublicationId)))))) (define tissue-short-name->id (cut string->identifier "tissue" <>)) -- cgit v1.2.3